Quorum Sensing Is a Language of Chemical Signals and Plays an Ecological Role in Algal-Bacterial Interactions

Algae are ubiquitous in the marine environment, and the ways in which they interact with bacteria are of particular interest in the field of marine ecology. The interactions between primary producers and bacteria impact the physiology of both partners, alter the chemistry of their environment, and shape microbial diversity. Although algal-bacterial interactions are well known and studied, information regarding the chemical-ecological role of this relationship remains limited, particularly with respect to quorum sensing (QS), which is a system of stimuli and response correlated to population density. In the microbial biosphere, QS is pivotal in driving community structure and regulating behavioral ecology, including biofilm formation, virulence, antibiotic resistance, swarming motility, and secondary metabolite production. Many marine habitats, such as the phycosphere, harbor diverse populations of microorganisms and various signal languages (such as QS-based autoinducers). QS-mediated interactions widely influence algal-bacterial symbiotic relationships, which in turn determine community organization, population structure, and ecosystem functioning. Understanding infochemicals-mediated ecological processes may shed light on the symbiotic interactions between algae host and associated microbes. In this review, we summarize current achievements about how QS modulates microbial behavior, affects symbiotic relationships, and regulates phytoplankton chemical-ecological processes. Additionally, we present an overview of QS-modulated co-evolutionary relationships between algae and bacterioplankton, and consider the potential applications and future perspectives of QS.     

Interactions among plants,bacteria, and fungi reduce extracellular enzyme activities under long‐term N fertilization

Atmospheric nitrogen (N) deposition has enhanced soil carbon (C) stocks in temperate forests. Most research has posited that these soil C gains are driven primarily by shifts in fungal community composition with elevated N leading to declines in lignin degrading Basidiomycetes. Recent research, however, suggests that plants and soil microbes are dynamically intertwined, whereby plants send C subsidies to rhizosphere microbes to enhance enzyme production and the mobilization of N. Thus, under elevated N, trees may reduce belowground C allocation leading to cascading impacts on the ability of microbes to degrade soil organic matter through a shift in microbial species and/or a change in plant–microbe interactions. The objective of this study was to determine the extent to which couplings among plant, fungal, and bacterial responses to N fertilization alter the activity of enzymes that are the primary agents of soil decomposition. We measured fungal and bacterial community composition, root–microbial interactions, and extracellular enzyme activity in the rhizosphere, bulk, and organic horizon of soils sampled from a long‐term (>25 years), whole‐watershed, N fertilization experiment at the Fernow Experimental Forest in West Virginia, USA. We observed significant declines in plant C investment to fine root biomass (24.7%), root morphology, and arbuscular mycorrhizal (AM) colonization (55.9%). Moreover, we found that declines in extracellular enzyme activity were significantly correlated with a shift in bacterial community composition, but not fungal community composition. This bacterial community shift was also correlated with reduced AM fungal colonization indicating that declines in plant investment belowground drive the response of bacterial community structure and function to N fertilization. Collectively, we find that enzyme activity responses to N fertilization are not solely driven by fungi, but instead reflect a whole ecosystem response, whereby declines in the strength of belowground C investment to gain N cascade through the soil environment.     

Plant functional traits and soil microbial biomass in different vegetation zones on the Loess Plateau

Plant functional traits built the relationships between plant diversity, species composition, and physiology along with the environmental changes, thus influencing soil microbial community. As the sensitivity indicators, soil microbial biomass and plant functional traits responses soil micro-organism and plant characteristics in direct way. Ten plant functional traits of 149 species and soil microbial biomass (carbon, nitrogen, and phosphorus) were analyzed across the different vegetation types (forest, forest-steppe, and steppe) that are divided by environmental gradient (temperature and precipitation), aimed to find the correlations among them. Our results confirmed the greatest values of plant functional traits (except the leaf density and the fine root density) that were distributed in the steppe zone, mainly due to the different mean annual temperature and mean annual precipitation conditions. For different plant growth forms, the plant functional traits were significant differences among the vegetation zones. The advantages of higher rate nutrient cycling, plentiful biomass supplements, and favorite habit conditions lead to the forest-steppe zone with the highest C_mic and N_mic concentrations. The canonical correlation analysis indicated that leaf nitrogen, root nitrogen, and fine root densities were correlated with root exudate and tissue which affected the concentrations of soil organic carbon (SOC) and total nitrogen (N), consequently impacting soil microbial biomass carbon (C_mic) and soil microbial biomass nitrogen (N_mic). Soil is the medium that connects micro-organism and plant root system that influenced leaf nitrogen, root nitrogen, and fine root density of plant functional traits, the concentrations of SOC and total N that plant feedback are consequently influencing C_mic and N_mic.     

Thirty-seven years of soil nitrogen and phosphorus fertility management shapes the structure and function of the soil microbial community in a Brown Chernozem

We tested whether levels of soil available nitrogen (N) and phosphorus (P) control the composition and function of the soil microbial community in a Brown Chernozemic soil on the Canadian Prairie. Soil dissolved organic carbon, N and P, and microbial communities structure (phospholipid fatty acid profile) and function (enzyme activity) were evaluated in the fallow and first wheat (Triticum aestivum L. cv. AC Eatonia) phases of fallow-wheat-wheat rotations where the wheat received soil test recommended rates of mineral N and P fertilizers (+N+P), or where N (?N+P) or P (+N?P) fertilizer use was withheld for 37 years. Differential fertilization modified soil N and P availability, and microbial community structure. Low N level was a major constraint when a rapidly growing wheat crop (heading stage) was drawing on the resource, reducing both plant N uptake and soil microbial biomass-C in ?N+P soils. Available P level in +N?P soils was about half that measured in P-fertilized soils, but P did not limit plant productivity or microbial development at that time. Changes in the microbial community structure seemingly buffered the impact of lower P availability in +N?P soils. Phosphatase activity was not involved, but increased abundance of arbuscular mycorrhizal fungi might be associated with this effect. Low soil N availability explained lower specific denitrification and higher specific nitrogenase activities in ?N+P soil growing wheat. Higher denitrification activity in +N+P soil could be attributed to higher soil C level and fertilization-induced shifts observed in the structure of the soil microbial community. Irrespective of the fertility level of the soil, all microbial communities grew at the relative growth rate of 17% day^?1 in a nutrient limitation assay that revealed no C, N or P limitation in these communities. We conclude that mineral fertilization, which modifies soil available N and P fertility, can be a selective force causing structural and functional shifts in the soil microbial community with a resulting impact on soil quality and nutrient fluxes.     

Nitrogen deposition weakens plant–microbe interactions in grassland ecosystems

Soil carbon (C) and nitrogen (N) stoichiometry is a main driver of ecosystem functioning. Global N enrichment has greatly changed soil C : N ratios, but how altered resource stoichiometry influences the complexity of direct and indirect interactions among plants, soils, and microbial communities has rarely been explored. Here, we investigated the responses of the plant‐soil‐microbe system to multi‐level N additions and the role of dissolved organic carbon (DOC) and inorganic N stoichiometry in regulating microbial biomass in semiarid grassland in northern China. We documented a significant positive correlation between DOC and inorganic N across the N addition gradient, which contradicts the negative nonlinear correlation between nitrate accrual and DOC availability commonly observed in natural ecosystems. Using hierarchical structural equation modeling, we found that soil acidification resulting from N addition, rather than changes in the plant community, was most closely related to shifts in soil microbial community composition and decline of microbial respiration. These findings indicate a down‐regulating effect of high N availability on plant–microbe interactions. That is, with the limiting factor for microbial biomass shifting from resource stoichiometry to soil acidity, N enrichment weakens the bottom‐up control of soil microorganisms by plant‐derived C sources. These results highlight the importance of integratively studying the plant‐soil‐microbe system in improving our understanding of ecosystem functioning under conditions of global N enrichment.     

Increased microbial functional diversity under long-term organic and integrated fertilization in a paddy soil

Microbes play key roles in diverse biogeochemical processes including nutrient cycling. However, responses of soil microbial community and functional genes to long-term integrated fertilization (chemical combined with organic fertilization) remain unclear. Here, we used pyrosequencing and a microarray-based GeoChip to explore the shifts of microbial community and functional genes in a paddy soil which received over 21-year fertilization with various regimes, including control (no fertilizer), rice straw (R), rice straw plus chemical fertilizer nitrogen (NR), N and phosphorus (NPR), NP and potassium (NPKR), and reduced rice straw plus reduced NPK (L-NPKR). Significant shifts of the overall soil bacterial composition only occurred in the NPKR and L-NPKR treatments, with enrichment of certain groups including Bradyrhizobiaceae and Rhodospirillaceae families that benefit higher productivity. All fertilization treatments significantly altered the soil microbial functional structure with increased diversity and abundances of genes for carbon and nitrogen cycling, in which NPKR and L-NPKR exhibited the strongest effect, while R exhibited the least. Functional gene structure and abundance were significantly correlated with corresponding soil enzymatic activities and rice yield, respectively, suggesting that the structural shift of the microbial functional community under fertilization might promote soil nutrient turnover and thereby affect yield. Overall, this study indicates that the combined application of rice straw and balanced chemical fertilizers was more pronounced in shifting the bacterial composition and improving the functional diversity toward higher productivity, providing a microbial point of view on applying a cost-effective integrated fertilization regime with rice straw plus reduced chemical fertilizers for sustainable nutrient management.

     

The effect of nutrient deposition on bacterial communities in Arctic tundra soil

The microbial communities of high‐latitude ecosystems are expected to experience rapid changes over the next century due to climate warming and increased deposition of reactive nitrogen, changes that will likely affect microbial community structure and function. In moist acidic tundra (MAT) soils on the North Slope of the Brooks Range, Alaska, substantial losses of C and N were previously observed after long‐term nutrient additions. To analyse the role of microbial communities in these losses, we utilized 16S rRNA gene tag pyrosequencing coupled with community‐level physiological profiling to describe changes in MAT bacterial communities after short‐ and long‐term nutrient fertilization in four sets of paired control and fertilized MAT soil samples. Bacterial diversity was lower in long‐term fertilized plots. The Acidobacteria were one of the most abundant phyla in all soils and distinct differences were noted in the distributions of Acidobacteria subgroups between mineral and organic soil layers that were also affected by fertilization. In addition, Alpha‐ and Gammaproteobacteria were more abundant in long‐term fertilized samples compared with control soils. The dramatic increase in sequences within the Gammaproteobacteria identified as Dyella spp. (order Xanthomonadales) in the long‐term fertilized samples was confirmed by quantitative PCR (qPCR) in several samples. Long‐term fertilization was also correlated with shifts in the utilization of specific substrates by microbes present in the soils. The combined data indicate that long‐term fertilization resulted in a significant change in microbial community structure and function linked to changes in carbon and nitrogen availability and shifts in above‐ground plant communities.     

Changa in the structure and activity of a soil microbial community caused by inorganic nitrogen fertilization

The changes in the structure and activity of a soil microbial community caused by addition of moderate and high rates of the mineral nitrogen fertilizer (KNO₃) were studied in a laboratory incubation experiment. The structure of the microbial community was evaluated from the phospholipid fatty acid (PLFA) profile; specific growth rate of the microorganisms was determined by the method of the kinetics of substrate-induced respiration; the total pool of microbial carbon was estimated by the fumigation-extraction method. The amounts of nitrogen fertilizer applied in three treatments of the experiment were 0 (control), 100, and 2000 ??g N/g soil. Even in the absence of additional sources of organic carbon, a considerable portion of the added ¹⁵N (up to 74%) was immobilized. No significant increase in the amount of microbial carbon was observed during incubation. The specific growth rate of the microbial community in soil supplemented with glucose decreased twofold after addition of 2000 ??g N/g soil. In this treatment, the ratio of cyclic fatty acids to their monoenoic precursors also increased, indicating the adaptation of microbial cells to extremely high amounts of nitrogen fertilizer. Moreover, considerable changes in the structure of the soil microbial community, such as an increase in the ratio of fungalto bacterial markers and a decrease in the ratio between PLFA of gram-positive and gram-negative bacteria, were observed in the treatment with addition of 2000 ??g N/g soil. Our data clearly indicate that mineral nitrogen fertilization of soil under carbon limitation has a pronounced impact on the structure and activity of soil microbial communities.     

Microbial community structure along an altitude gradient in three different localities

The microbial community structure along an altitude gradient was investigated in different localities, in Kalasi lake, Urumqi river and Sangong river, Xingjiang (China). The mean numbers of DAPI (4',6-diamidino-2-phenylindole)-stained cells were lower in Kalasi lake than that in Urumqi river and Sangong river; these differences were attributed to increasing environmental harshness including lower soil organic carbon and nitrogen content, more acidic pH and lower annual temperature. In each locality, the numbers of bacteria and archaea measured with two fluorescence-labeled 16S rRNA oligonucleotide probes (EUB338 and ARCH915) were higher in a coniferous forest and lower in desert vegetation. A significant and positive relationship was found between microbial and soil organic carbon and total nitrogen along the altitudinal gradient, indicating that plant communities and soil nutrients influence the soil microbial structure. The results show that the microbial population in higher latitudinal site was fewer than lower latitudinal one, soil microorganisms were positively correlated to soil organic carbon and total nitrogen, and plant communities had an obviously impact on soil microbes.     

土地利用驱动的土壤性状变化影响微生物群落结构和功能

微生物在调节陆地生态系统地球化学循环过程中具有重要作用。土地利用方式改变显著影响土壤微生物群落结构和功能,但对土地利用驱动的土壤性状变化与微生物群落结构和功能关系的研究相对匮乏。依托长期定位监测试验（始于1984年）,通过16S rRNA基因片段和ITS高通量测序,研究了土地利用方式（裸地、农田、草地）驱动的土壤碳氮变化对微生物群落结构和功能的影响。结果表明：对于细菌群落而言,裸地中α-多样性最高、其次是草地、农田中最低,农田和草地中细菌优势菌群变形菌（Proteobacteria）和放线菌门（Actinobacteria）相对丰度较裸地低4.5%、3.9%和5.5%、3.8%;对于真菌群落而言,裸地子囊菌门（Ascomycota）相对丰度最高、农田次之、草地最低;化能异养型、好氧化能异养型细菌相对丰度裸地显著高于农田和草地（P<0.05）,而硝化型和好氧氨氧化型细菌裸地显著低于农田和草地（P<0.05）;腐生型真菌相对丰度大小排序为：裸地>农田>草地。细菌群落变化主要与土壤容重、全氮、矿质氮、C ： N比和微生物量碳有关,而真菌群落与土壤矿质氮有关。细菌和真菌功能菌群主要受土壤容重、土壤有机碳、土壤全氮、C ： N比和微生物量碳影响。因此,土壤容重、土壤全氮、土壤有机碳、C ： N比、微生物量碳、矿质氮差异可能是影响不同土地利用方式中微生物群落和功能变化的主要因素。     

微生物对分解底物碳氮磷化学计量的响应和调节机制

微生物分解者的生存和生长策略、群落结构和功能会随着底物化学计量特征而改变, 从而强烈地影响底物的分解速度和元素的周转速率, 进而影响生态系统的功能过程。深入理解微生物生理代谢活动和群落结构与陆地生态系统过程之间的联系及其对全球变化的响应和反馈机理是生态学和全球变化生物学领域值得关注的重大科学命题。该文基于生态化学计量学理论和代谢理论, 首先介绍微生物在陆地生态系统碳氮磷循环中的作用; 然后综述微生物对分解底物化学计量变异性的响应和调节的4种主要机制: (1)调整微生物自身化学计量特征; (2)调整微生物群落结构; (3)产生特定的胞外酶以获取受限制的资源; (4)改变碳氮磷元素利用效率。最后, 通过分析当前研究不足, 提出该领域亟需关注的科学问题有: (1)综合阐明微生物对底物化学计量变化响应的各种机制及其相对重要性; (2)探索全球变化对微生物驱动的碳氮磷循环的影响; (3)探索微生物对底物化学计量变化适应对策的时空变化。     

Responses and regulation mechanisms of microbial decomposers to substrate carbon,nitrogen, and phosphorus stoichiometry

The survival and growth strategies, community structure and functions of microbial decomposers vary with substrate stoichiometry, which profoundly influences substrate decomposition, turnover, and hence the carbon and nutrient cycles of terrestrial ecosystems. It is crucial to understand the relationships among microbial metabolism, community structure and ecosystem processes of terrestrial ecosystems and their responses and feedbacks to global changes. In this review, we first introduced the significance of microbial decomposers in the carbon, nitrogen, and phosphorus cycles of terrestrial ecosystems from perspectives of ecological stoichiometry and metabolic theories. Then we synthesized four potential mechanisms of microbial response and control on substrate stoichiometric variations, i.e., through (1) modifying microbial stoichiometry, (2) shifting microbial community structure, (3) producing extracellular enzymes to acquire limiting resources, and (4) changing microbial carbon, nitrogen, and phosphor use efficiencies. Finally, we proposed three research directions in this field: (1) to comprehensively explore various microbial mechanisms in response to changes in substrate stoichiometry and the relative importance of these mechanisms; (2) to examine influences of global changes on microbial-driven cycles of carbon, nitrogen, and phosphorus; and (3) to explore spatiotemporal changes in the strategies of microbial adaptation to changes in the substrate stoichiometry.     

Changes in Microbial Plankton Assemblages Induced by Mesoscale Oceanographic Features in the Northern Gulf of Mexico

Mesoscale circulation generated by the Loop Current in the Northern Gulf of Mexico (NGOM) delivers growth-limiting nutrients to the microbial plankton of the euphotic zone. Consequences of physicochemically driven community shifts on higher order consumers and subsequent impacts on the biological carbon pump remain poorly understood. This study evaluates microbial plankton <10 μm abundance and community structure across both cyclonic and anti-cyclonic circulation features in the NGOM using flow cytometry (SYBR Green I and autofluorescence parameters). Non-parametric multivariate hierarchical cluster analyses indicated that significant spatial variability in community structure exists such that stations that clustered together were defined as having a specific ‘microbial signature’ (i.e. statistically homogeneous community structure profiles based on relative abundance of microbial groups). Salinity and a combination of sea surface height anomaly and sea surface temperature were determined by distance based linear modeling to be abiotic predictor variables significantly correlated to changes in microbial signatures. Correlations between increased microbial abundance and availability of nitrogen suggest nitrogen-limitation of microbial plankton in this open ocean area. Regions of combined coastal water entrainment and mesoscale convergence corresponded to increased heterotrophic prokaryote abundance relative to autotrophic plankton. The results provide an initial assessment of how mesoscale circulation potentially influences microbial plankton abundance and community structure in the NGOM.     

Tight Coupling Between Shoot Level Foliar N and P,Leaf Area,and Shoot Growth in Arctic Dwarf Shrubs Under Simulated Climate Change

Nutrient availability limits productivity of arctic ecosystems, and this constraint means that the amount of nitrogen (N) in plant canopies is an exceptionally strong predictor of vegetation productivity. However, climate change is predicted to increase nutrient availability leading to increases in carbon sequestration and shifts in community structure to more productive species. Despite tight coupling of productivity with canopy nutrients at the vegetation scale, it remains unknown how species/shoot level foliar nutrients couple to growth, or how climate change may influence foliar nutrients–productivity relationships to drive changes in ecosystem carbon gain and community structure. We investigated the influence of climate change on arctic plant growth relationships to shoot level foliar N and phosphorus (P) in three dominant subarctic dwarf shrubs using an 18-year warming and nutrient addition experiment. We found a tight coupling between total leaf N and P per shoot, leaf area and shoot extension. Furthermore, a steeper shoot length-leaf N relationship in deciduous species (Vaccinium myrtillus and Vaccinium uliginosum) under warming manipulations suggests a greater capacity for nitrogen to stimulate growth under warmer conditions in these species. This mechanism may help drive the considerable increases in deciduous shrub cover observed already in some arctic regions. Overall, our work provides the first evidence at the shoot level of tight coupling between foliar N and P, leaf area and growth i.e. consistent across species, and provides mechanistic insight into how interspecific differences in alleviation of nutrient limitation will alter community structure and primary productivity in a warmer Arctic.     

Microbial Biomass and Community Structure in a Sequence of Soils with Increasing Fertility and Changing Land Use

Abstract The microbial biomass and community structure of eight Chinese red soils with different fertility and land use history was investigated. Two community based microbiological measurements, namely, community level physiological profiling (CLPP) using Biolog sole C source utilization tests and phospholipid fatty acid (PLFA) profiles, were used to investigate the microbial ecology of these soils and to determine how land use alters microbial community structure. Microbial biomass-C and total PLFAs were closely correlated to organic carbon and total nitrogen, indicating that these soil microbial measures are potentially good indices of soil fertility in these highly weathered soils. Metabolic quotients and C source utilization were not correlated with organic carbon or microbial biomass. Multivariate analysis of sole carbon source utilization patterns and PLFAs demonstrated that land use history and plant cover type had a significant impact on microbial community structure. PLFAs showed these differences more than CLPP methods. Consequently, PLFA analysis was a better method for assessing broad-spectrum community differences and at the same time attempting to correlate changes with soil fertility. Soils from tea orchards were particularly distinctive in their CLPP. A modified CLPP method, using absorbance readings at 405 nm and different culture media at pH values of 4.7 and 7.0, showed that the discrimination obtained can be influenced by the culture conditions. This method was used to show that the distinctive microbial community structure in tea orchard soils was not, however, due to differences in pH alone. Received: 1 December 1999; Accepted: 6 June 2000; Online Publication: 28 August 2000     

Urban Stormwater Runoff Drives Denitrifying Community Composition Through Changes in Sediment Texture and Carbon Content

The export of nitrogen from urban catchments is a global problem, and denitrifying bacteria in stream ecosystems are critical for reducing in-stream N. However, the environmental factors that control the composition of denitrifying communities in streams are not well understood. We determined whether denitrifying community composition in sediments of nine streams on the eastern fringe of Melbourne, Australia was correlated with two measures of catchment urban impact: effective imperviousness (EI, the proportion of a catchment covered by impervious surfaces with direct connection to streams) or septic tank density (which affects stream water chemistry, particularly stream N concentrations). Denitrifying community structure was examined by comparing terminal restriction fragment length polymorphisms of nosZ genes in the sediments, as the nosZ gene codes for nitrous oxide reductase, the last step in the denitrification pathway. We also determined the chemical and physical characteristics of the streams that were best correlated with denitrifying community composition. EI was strongly correlated with community composition and sediment physical and chemical properties, while septic tank density was not. Sites with high EI were sandier, with less fine sediment and lower organic carbon content, higher sediment cations (calcium, sodium and magnesium) and water filterable reactive phosphorus concentrations. These were also the best small-scale environmental variables that explained denitrifying community composition. Among our study streams, which differed in the degree of urban stormwater impact, sediment grain size and carbon content are the most likely drivers of change in community composition. Denitrifying community composition is another in a long list of ecological indicators that suggest the profound degradation of streams is caused by urban stormwater runoff. While the relationships between denitrifying community composition and denitrification rates are yet to be unequivocally established, landscape-scale indices of environmental impact such as EI may prove to be useful indicators of change in microbial communities.     

Ecoenzymatic Stoichiometry in Relation to Productivity for Freshwater Biofilm and Plankton Communities

The degradation of detrital organic matter and assimilation of carbon (C), nitrogen (N), and phosphorus (P) by heterotrophic microbial communities is mediated by enzymes released into the environment (ecoenzymes). For the attached microbial communities of soils and freshwater sediments, the activities of β-glucosidase, β-N-acetylglucosaminidase, leucine aminopeptidase, and phosphatase show consistent stoichiometric patterns. To determine whether similar constraints apply to planktonic communities, we assembled data from nine studies that include measurements of these enzyme activities along with microbial productivity. By normalizing enzyme activity to productivity, we directly compared the ecoenzymatic stoichiometry of aquatic biofilm and bacterioplankton communities. The relationships between β-glucosidase and α-glucosidase and β-glucosidase and β-N-acetylglucosaminidase were statistically indistinguishable for the two community types, while the relationships between β-glucosidase and phosphatase and β-glucosidase and leucine aminopeptidase significantly differed. For β-glucosidase vs. phosphatase, the differences in slope (biofilm 0.65, plankton 1.05) corresponded with differences in the mean elemental C:P ratio of microbial biomass (60 and 106, respectively). For β-glucosidase vs. leucine aminopeptidase, differences in slope (0.80 and 1.02) did not correspond to differences in the mean elemental C:N of biomass (8.6 and 6.6). β-N-Acetylglucosaminidase activity in biofilms was significantly greater than that of plankton, suggesting that aminosaccharides were a relatively more important N source for biofilms, perhaps because fungi are more abundant. The slopes of β-glucosidase vs. (β-N-acetylglucosaminidase + leucine aminopeptidase) regressions (biofilm 1.07, plankton 0.94) corresponded more closely to the estimated difference in mean biomass C:N. Despite major differences in physical structure and trophic organization, biofilm and plankton communities have similar ecoenzymatic stoichiometry in relation to productivity and biomass composition. These relationships can be integrated into the stoichiometric and metabolic theories of ecology and used to analyze community metabolism in relation to resource constraints.     

Comparative metagenomic,phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients

Terrestrial ecosystems are receiving elevated inputs of nitrogen (N) from anthropogenic sources and understanding how these increases in N availability affect soil microbial communities is critical for predicting the associated effects on belowground ecosystems. We used a suite of approaches to analyze the structure and functional characteristics of soil microbial communities from replicated plots in two long-term N fertilization experiments located in contrasting systems. Pyrosequencing-based analyses of 16S rRNA genes revealed no significant effects of N fertilization on bacterial diversity, but significant effects on community composition at both sites; copiotrophic taxa (including members of the Proteobacteria and Bacteroidetes phyla) typically increased in relative abundance in the high N plots, with oligotrophic taxa (mainly Acidobacteria) exhibiting the opposite pattern. Consistent with the phylogenetic shifts under N fertilization, shotgun metagenomic sequencing revealed increases in the relative abundances of genes associated with DNA/RNA replication, electron transport and protein metabolism, increases that could be resolved even with the shallow shotgun metagenomic sequencing conducted here (average of 75 000 reads per sample). We also observed shifts in the catabolic capabilities of the communities across the N gradients that were significantly correlated with the phylogenetic and metagenomic responses, indicating possible linkages between the structure and functioning of soil microbial communities. Overall, our results suggest that N fertilization may, directly or indirectly, induce a shift in the predominant microbial life-history strategies, favoring a more active, copiotrophic microbial community, a pattern that parallels the often observed replacement of K-selected with r-selected plant species with elevated N.     

Microbial community shifts influence patterns in tropical forest nitrogen fixation

The role of biodiversity in ecosystem function receives substantial attention, yet despite the diversity and functional relevance of microorganisms, relationships between microbial community structure and ecosystem processes remain largely unknown. We used tropical rain forest fertilization plots to directly compare the relative abundance, composition and diversity of free-living nitrogen (N)-fixer communities to in situ leaf litter N fixation rates. N fixation rates varied greatly within the landscape, and ‘hotspots’ of high N fixation activity were observed in both control and phosphorus (P)-fertilized plots. Compared with zones of average activity, the N fixation ‘hotspots’ in unfertilized plots were characterized by marked differences in N-fixer community composition and had substantially higher overall diversity. P additions increased the efficiency of N-fixer communities, resulting in elevated rates of fixation per nifH gene. Furthermore, P fertilization increased N fixation rates and N-fixer abundance, eliminated a highly novel group of N-fixers, and increased N-fixer diversity. Yet the relationships between diversity and function were not simple, and coupling rate measurements to indicators of community structure revealed a biological dynamism not apparent from process measurements alone. Taken together, these data suggest that the rain forest litter layer maintains high N fixation rates and unique N-fixing organisms and that, as observed in plant community ecology, structural shifts in N-fixing communities may partially explain significant differences in system-scale N fixation rates.